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- PDB-6zjh: Trehalose transferase from Thermoproteus uzoniensis soaked with t... -

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Basic information

Entry
Database: PDB / ID: 6zjh
TitleTrehalose transferase from Thermoproteus uzoniensis soaked with trehalose
ComponentsTrehalose phosphorylase/synthase
KeywordsTRANSFERASE / trehalose transferase / retaining glycosyltransferase / glycosidic bond formation
Function / homology: / : / Trehalose synthase, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / glucose metabolic process / trehalose / Trehalose phosphorylase/synthase
Function and homology information
Biological speciesThermoproteus uzoniensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBento, I. / Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.-H. / Hanefeld, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
European CommissionERA-IB-15-110 Germany
CitationJournal: Acs Catalysis / Year: 2020
Title: Anomeric Selectivity of Trehalose Transferase with Rare l-Sugars.
Authors: Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.L. / Bento, I. / Hanefeld, U.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Trehalose phosphorylase/synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9383
Polymers45,5031
Non-polymers4342
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint8 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.433, 68.387, 110.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Trehalose phosphorylase/synthase


Mass: 45503.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus uzoniensis (strain 768-20) (archaea)
Strain: 768-20 / Gene: TUZN_0976 / Production host: Escherichia coli (E. coli) / References: UniProt: F2L613
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationMonochromator: double-crystal monochromator (DCM) FMB-OXFORD (Oxford, UK)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→110.75 Å / Num. obs: 27421 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.048 / Rrim(I) all: 0.088 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-110.755.10.0264330.9990.0160.031
2.1-2.1661.57621990.51.0291.889

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-Tret

Resolution: 2.1→58.188 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.185 / SU B: 7.794 / SU ML: 0.185 / Average fsc free: 0.8302 / Average fsc work: 0.8439 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2445 1381 5.046 %
Rwork0.1997 25989 -
all0.202 --
obs-27370 99.535 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.412 Å2
Baniso -1Baniso -2Baniso -3
1-3.211 Å20 Å2-0 Å2
2---3.559 Å20 Å2
3---0.347 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 29 91 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173180
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.6544443
X-RAY DIFFRACTIONr_angle_other_deg1.1331.5897320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67521.229179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88915571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7241527
X-RAY DIFFRACTIONr_chiral_restr0.0550.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
X-RAY DIFFRACTIONr_nbd_refined0.1870.2608
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.22987
X-RAY DIFFRACTIONr_nbtor_refined0.1550.21556
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2117
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.26
X-RAY DIFFRACTIONr_nbd_other0.1590.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.22
X-RAY DIFFRACTIONr_mcbond_it2.6615.3121576
X-RAY DIFFRACTIONr_mcbond_other2.665.311575
X-RAY DIFFRACTIONr_mcangle_it4.1197.9611967
X-RAY DIFFRACTIONr_mcangle_other4.1197.9641968
X-RAY DIFFRACTIONr_scbond_it3.1115.7941705
X-RAY DIFFRACTIONr_scbond_other3.115.7951706
X-RAY DIFFRACTIONr_scangle_it5.0698.5062475
X-RAY DIFFRACTIONr_scangle_other5.0688.5072476
X-RAY DIFFRACTIONr_lrange_it6.89661.5443539
X-RAY DIFFRACTIONr_lrange_other6.88561.493524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.352920.34618840.34719940.510.51199.09730.33
2.154-2.2130.331030.32518460.32519620.60.57799.33740.307
2.213-2.2780.3281100.28217840.28519100.7230.72199.16230.254
2.278-2.3480.3491040.26217160.26718250.7560.8199.7260.234
2.348-2.4240.281830.26716890.26817800.8440.83499.55060.238
2.424-2.5090.304830.24516430.24817330.8340.87199.59610.213
2.509-2.6040.311840.2415890.24416780.8680.88299.7020.21
2.604-2.710.291950.23315050.23616050.880.89899.68850.202
2.71-2.830.268700.21214860.21515600.9240.92799.74360.183
2.83-2.9680.309730.20713930.21114690.9120.93299.79580.185
2.968-3.1280.291730.22213490.22514300.9020.91499.44060.204
3.128-3.3170.303700.23112790.23413500.8790.91199.92590.211
3.317-3.5450.213490.2112080.2112650.9370.93999.36760.199
3.545-3.8280.22560.18211390.18412000.9430.95899.58330.176
3.828-4.1920.17510.16110270.16110820.9640.96499.63030.16
4.192-4.6840.207580.1549470.15710100.9580.96899.50490.157
4.684-5.4020.245420.1528330.1568830.960.97299.0940.154
5.402-6.6020.236430.1877280.197720.9430.95999.87050.19
6.602-9.2770.141240.1385910.1386160.9750.97999.83770.146
9.277-58.1880.177180.23530.1993740.9740.96799.19790.207

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